PGK2

phosphoglycerate kinase 2

Basic information

Region (hg38): 6:49785660-49787285

Links

ENSG00000170950 ∙ NCBI:5232 ∙ OMIM:172270 ∙ HGNC:8898 ∙ Uniprot:P07205 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PGK2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGK2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			41			41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	0	0

Variants in PGK2

This is a list of pathogenic ClinVar variants found in the PGK2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-49785945-T-A		not specified	Uncertain significance (Jan 16, 2024)
6-49786023-C-G		not specified	Uncertain significance (Nov 26, 2024)
6-49786028-T-C		not specified	Uncertain significance (Jan 04, 2022)
6-49786098-A-G		not specified	Uncertain significance (Jul 25, 2023)
6-49786100-G-A		not specified	Uncertain significance (Jan 09, 2025)
6-49786172-G-A		not specified	Uncertain significance (Dec 19, 2023)
6-49786217-T-C		not specified	Uncertain significance (Aug 19, 2024)
6-49786225-G-T		not specified	Uncertain significance (Dec 13, 2023)
6-49786229-C-T		not specified	Uncertain significance (Dec 17, 2023)
6-49786238-C-A		not specified	Uncertain significance (Jun 06, 2023)
6-49786434-C-T		not specified	Uncertain significance (May 02, 2024)
6-49786446-G-A		not specified	Uncertain significance (Jul 14, 2022)
6-49786473-C-G		not specified	Uncertain significance (Aug 27, 2024)
6-49786490-T-C		not specified	Uncertain significance (Dec 07, 2024)
6-49786507-C-T		not specified	Uncertain significance (Dec 28, 2023)
6-49786514-T-C		not specified	Uncertain significance (Oct 20, 2024)
6-49786540-T-A		not specified	Uncertain significance (Aug 14, 2023)
6-49786560-C-A		not specified	Uncertain significance (Aug 05, 2024)
6-49786650-T-C		not specified	Uncertain significance (Nov 17, 2022)
6-49786674-C-T		not specified	Uncertain significance (Nov 09, 2021)
6-49786676-C-T		not specified	Uncertain significance (Nov 20, 2024)
6-49786677-G-A		not specified	Uncertain significance (May 30, 2023)
6-49786707-A-G		not specified	Uncertain significance (Mar 10, 2025)
6-49786753-A-T		not specified	Uncertain significance (Dec 21, 2022)
6-49786785-G-T		not specified	Uncertain significance (Sep 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGK2	protein_coding	protein_coding	ENST00000304801	1	1688

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000968	0.348	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.921	257	219	1.18	0.0000111	2747
Missense in Polyphen		79	76.778	1.0289		971
Synonymous	-1.68	101	81.7	1.24	0.00000449	850
Loss of Function	0.242	8	8.77	0.912	5.50e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential for sperm motility and male fertility (PubMed:26677959). Not required for the completion of spermatogenesis (By similarity). {ECO:0000250|UniProtKB:P09041, ECO:0000269|PubMed:26677959}.
• Pathway: Glycolysis / Gluconeogenesis - Homo sapiens (human);Cori Cycle;Pathways in clear cell renal cell carcinoma;Glycolysis and Gluconeogenesis;Metabolism of carbohydrates;Glycolysis Gluconeogenesis;Glycolysis and Gluconeogenesis;Metabolism;Glycolysis;gluconeogenesis;glycolysis;superpathway of conversion of glucose to acetyl CoA and entry into the TCA cycle;Gluconeogenesis;Glucose metabolism (Consensus)

Recessive Scores

• pRec: 0.503

Intolerance Scores

• loftool: 0.165
• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.06

Haploinsufficiency Scores

• pHI: 0.504
• hipred: N
• hipred_score: 0.248
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.966

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pgk2
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: gluconeogenesis;glycolytic process;phosphorylation;positive regulation of oxidative phosphorylation
• Cellular component: nucleus;cytosol;sperm fibrous sheath;extracellular exosome
• Molecular function: phosphoglycerate kinase activity;ATP binding;ADP binding